We molecularly characterized samples with Giardia , Cryptosporidium , and soil-transmitted helminths from a facility-based surveillance system for diarrhea in Santa Rosa, Guatemala. The DNA sequence analysis determined the presence of Giardia assemblages A ( N = 7) and B ( N = 12) and, Cryptosporidium hominis ( N = 2) and Cryptosporidium parvum ( N = 2), suggestive of different transmission cycles. All 41 samples with soil-transmitted helminths did not have the β-tubulin mutation described for benzimidazole resistance, suggesting potential usefulness in mass drug administration campaigns.