To determine whether the presence of Blastocystis is associated with other gastrointestinal parasite infections, stool samples from 95 Honduran rural children were analyzed using multi-parallel quantitative real-time polymerase chain reaction (PCR) and Kato-Katz. Combined results detected the following prevalence: Blastocystis, 71.6%; Trichuris trichiura, 63.2%; Giardia lamblia, 40.0%; Ascaris lumbricoides, 15.8%; and Necator americanus, 4.2%. Age was found associated with the quantity of both Blastocystis DNA (r s = 0.524, P < 0.001) and T. trichiura DNA in the stool (fg/µL) by quantitative PCR (r s = 0.272, P < 0.001). In addition, there was an association with T. trichiura and Blastocystis infection (odds ratio [OR] = 4.72; 95% CI = 1.83, 12.20; P < 0.001). These findings demonstrate a high prevalence of Blastocystis and other intestinal parasites in a rural location in Honduras.