Walther Kruse is remembered for his work in parasitology and his research of intestinal bacteria infections. He performed extensive studies of Shigella dysenteriae during an epidemic of dysentery in the Ruhr area of Germany. This organism is sometimes referred to as the "Shiga-Kruse bacillus", and its associated disease as "Shiga-Kruse dysentery". These eponyms are shared with Japanese bacteriologist Kiyoshi Shiga (1871-1957). Kruse documented his findings in a 1900 treatise titled Über die Ruhr als Volkskrankheit und ihren Erreger.
In 1914 he demonstrated that the common cold could be transmitted to healthy individuals via nasal secretions that were free of bacteria. The results of these experiments were published in a treatise called Die Erreger von Husten und Schnopfen. Also, a specialized tool used to spread material over the surface of a culture medium is called "Kruse's brush".