The largest cities in terms of population in the United States that begin with "San" are San Antonio in Texas and San Diego, San Francisco and San Jose in California. Many other states have smaller cities that begin with "San" as well.
Cities prefixed with "San" are most common in the southwestern states, particularly in California. California has many other cities that begin with "San" such as San Bernardino, San Bruno, San Leandro, San Luis Obispo, San Mateo and San Rafael. Texas has 10 cities beginning with "San", including San Juan, San Marcos and San Perlita. Arizona and Colorado each have a San Luis and New Mexico has San Felipe Pueblo, San Ysidro and San Miguel.
The prefix "San" is also common in the regions of the country that were originally held by Mexico. In Spanish, "san" means "saint" and it is a common naming convention for populated areas. While the use of "San" is more common in the westernmost states, it is not entirely exclusive to them. Florida has a city of San Antonio of its own. The territory of Puerto Rico also naturally has a number of "San" cities such as San Juan, San German and San Sebastian.