Twelve sulfonamide residues, namely, sulfadiazine, sulfamerazine, sulfamethazine, sulfamonomethoxine, sulfadoxine, sulfamethoxazole, sulfaquinoxaline, sulfadimethoxine, sulfanilamide, sulfathiazole, sulfapyridine, and sulfamethizole were determined in pork tissue, chicken, and eggs by ultra-performance LC/MS/MS after SPE cleanup using multiwalled carbon nanotubes, which permitted extracted samples from animal tissue and eggs to be cleaned up under either normal phase (NP) or reversed phase (RP) conditions or both. In this method, the NP cleanup provided recoveries for nine of the 12 sulfonamides ranging from 71 to 90% and <60% for the remaining three with RSDs lower than 10%. For the RP cleanup method, the recoveries for nine of the 12 sulfonamides ranged from 70 to 94% and <60% for the remaining three with RSDs <11.1%. The two cleanup methods can complement each other to complete the simultaneous analysis of the 12 sulfonamides.