In Neolithic Europe, the Swiss plateau was dominated by the Linear Pottery culture from the 5th millennium BC; it lay on the south-western outskirts of the Corded Ware horizon in the 3rd millennium BC, evolving into the early Bronze Age Beaker culture. Artefacts dated to the 5th millennium BC were discovered at the Schnidejoch in 2003 to 2005. The first Indo-European settlement likely dates to the 2nd millennium, at the latest in the form of the Urnfield culture from c. 1300 BC. The Swiss plateau lay in the western part of the pre- or proto-Celtic Halstatt culture, evolving into the Celtic La Tène culture from the 5th century BC. In the 1st century BC (late La Tène), the Swiss plateau was occupied by the Helvetii in the west and by the Vindelici in the east, while the Alpine parts of eastern Switzerland were inhabited by the Raetians.
In 58 BCE, the Helvetii tried to evade migratory pressure from Germanic tribes by moving into Gaul, but were stopped and defeated at Bibracte (near modern-day Autun) by Julius Caesar's armies and then sent back. In 15 BCE, Tiberius and Drusus conquered the Alps, and the region became integrated into the Roman Empire: the Helvetii settlement area became part first of Gallia Belgica and later of the province of Germania Superior, while the eastern part was integrated into the Roman province of Raetia.
The following 300 years saw extensive Roman settlement, including the construction of a road network and the founding of many settlements and cities. The center of Roman occupation was at Aventicum (Avenches), other cities were founded at Arbor Felix (Arbon), Augusta Raurica (Kaiseraugst near Basel), Basilea (Basel), Curia (Chur), Genava (Genève), Lousanna (Lausanne), Octodurum (Martigny, controlling the pass of the Great St. Bernard), Salodurum (Solothurn), Turicum (Zürich) and other places. Military garrisons existed at Tenedo (Zurzach) and Vindonissa (Windisch).
The Romans also developed the Great St. Bernard Pass beginning in the year 47, and in 69 part of the legions of Vitellius used it to traverse the Alps. (It is doubtful whether Hannibal, in the Second Punic War some 300 years earlier, had crossed the alps over the Great St. Bernhard. Historians believe today that he had traveled over a lower and more southerly pass in the Alps between Lake Geneva and the Mediterranean Sea.)
In 259, Alamanni tribes overran the Limes and caused widespread devastation of Roman cities and settlements. The Roman empire managed to reestablish the Rhine as the border, and the cities on Swiss territory were rebuilt. However, it was now a frontier province, and consequently the new Roman cities were smaller and much more fortified.
The first bishoprics were founded in the 4th and 5th century in Basel (documented in 346), Martigny (doc. 381, moved to Sion in 585), Geneva (doc. 441), and Chur (doc. 451). There is evidence from the 6th century for a bishopric in Lausanne, which maybe had been moved from Avenches.
With the fall of the Western Roman Empire, Germanic tribes moved in. Burgundians settled in the Jura, the Rhône valley and the Alps south of Lake Geneva; while in the north, Alamannic settlers crossed the Rhine in 406 and slowly assimilated the Gallo-Roman population, or made it retreat into the mountains. Burgundy became a part of the Frankish kingdom in 534; two years later, the dukedom of Alemannia followed suit.
The Burgundy kings furthered the Christianization through newly founded monasteries, e.g. at Romanmôtier or St. Maurice in the Valais in 515. In the Alaman part, only isolated Christian communities continued to exist; the Germanic faith including the worship of Wuodan was prevalent. The Irish monks Columbanus and Gallus re-introduced Christian faith in the early 7th century. The Bishopric of Konstanz also was founded at that time.
Under the Carolingian kings, the feudal system proliferated, and monasteries and bishopries were important bases for maintaining the rule. The Treaty of Verdun of 843 assigned the western part of modern Switzerland (Upper Burgundy) to Lotharingia, ruled by Lothair I, and the eastern part (Alemannia) to the eastern kingdom of Louis the German that would become the Holy Roman Empire. The boundary between Alamania, ruled by Louis, and western Burgundy, ruled by Lothar, ran along the lower Aare, turning towards the south at the Rhine, passing west of Lucerne and across the Alps along the upper Rhône to Saint Gotthard Pass.
Louis the German in 853 assigned a monastery in Zürich as the Fraumünster to his daughter Hildegard. According to legend this occurred after a stag bearing an illuminated crucifix between his antlers appeared to him in the marshland outside the town, at the shore of Lake Zürich. However, there is evidence that the monastery was already in existence before 853. The Fraumünster is across the river from the Grossmünster, which according to legend was founded by Charlemagne himself, as his horse fell to his knees on the spot where the martyrs Felix and Regula were buried.
In the 10th century, the rule of the Carolingians waned: Magyars destroyed Basel in 917 and St. Gallen in 926, and Saracenes ravaged the Valais after 920 and sacked the monastery of St. Maurice in 939. The Conradines (von Wetterau) started a long time rule over Swabia during this time. Only after the victory of king Otto I over the Magyars in 955 in the Battle of Lechfeld were the Swiss territories reintegrated into the empire.
King Rudolph III of the Arelat kingdom (r. 993–1032) gave the Valais as his fiefdom to the Bishop of Sion in 999, and when Burgundy and thus also the Valais became part of the Holy Roman Empire in 1032, the bishop was also appointed count of the Valais. The Arelat mostly existed on paper throughout the 11th to 14th centuries, its remnants passing to France in 1378, but without its Swiss portions, Berne and Aargau having come under Zähringer and Habsburg rule already by the 12th cenrtury, and the County of Savoy was detached from the Arelat just before its dissolution, in 1361.
The dukes of Zähringen founded many cities, the most important being Freiburg in 1120, Fribourg in 1157, and Berne in 1191. The Zähringer dynasty ended with the death of Berchtold V in 1218, and their cities subsequently thus became independent, while the dukes of Kyburg competed with the house of Habsburg over control of the rural regions of the former Zähringer territory.
Under the Hohenstaufen rule, the alpine passes in Raetia and the St. Gotthard Pass gained importance. Especially the latter became an important direct route through the mountains. The construction of the "Devil’s Bridge" (Teufelsbrücke) across the Schöllenenschlucht in 1198 led to a marked increase in traffic on the mule track over the pass. Frederick II accorded the Reichsfreiheit to Schwyz in 1240 in the Freibrief von Faenza in an attempt to place the important pass under his direct control, and his son and for some time co-regent Henry VII had already given the same privileges to the valley of Uri in 1231 (the Freibrief von Hagenau). Unterwalden was de facto realm-free, since most of its territory belonged to monasteries, which had become independent even earlier in 1173 under Frederick I "Barbarossa" and in 1213 under Frederick II. The city of Zürich became reichsfrei in 1218.
The rise of the Habsburg dynasty gained momentum when their main local competitor, the Kyburg dynasty, died out and they could thus bring much of the territory south of the Rhine under their control. Subsequently, they managed within only a few generations to extend their influence through Swabia in south-eastern Germany to Austria. Rudolph I of Habsburg, who became emperor of the Holy Roman Empire in 1273, instituted a strict rule in his homelands and raised the taxes tremenduously to finance wars and further territorial acquisitions. As king, he finally had also become the direct liege lord of the "Forest Communities" (Waldstätten, i.e. Uri, Schwyz, and Unterwalden), which thus saw their previous independence curtailed.
In the Valais, increasing tensions between the bishops of Sion and the Counts of Savoy led to a war beginning in 1260. The war ended after the Battle at the Scheuchzermatte near Leuk in 1296, where the Savoy forces were crushed by the bishop's army, supported by forces from Berne. After the peace of 1301, Savoy kept only the lower part of the Valais, while the bishop controlled the upper Valais.