Objective: To evaluate the frequency of intestinal parasites and risk factors associated with coccidian infection in patients cared for at a public hospital in Lima-Peru. Methods: A descriptive, cross-sectional study was conducted using reports of the parasitology laboratory. Patients included were >18 years, who gave at least one faecal sample for parasitologic evaluation. Logistic regression was used to calculate Odd Ratios (OR) and 95% confidence intervals. Results: 2.056 patients were included in the analysis, 55.2% of them were males and 334 (16.3%) were HIV positive. Overall, Blastocystis hominis was the most frequent parasite (35.4%). The multivariate model adjusted for sex shows that HIV infection (OR = 4.53; 95%CI: 3.03-6.77), being hospitalized (OR = 2.42; 95%CI: 1.06-5.52), and age ≥ 40 years (OR = 0.57; 95%IC: 0.37-0.86) were associated with coccidian infection. Conclusions: Blastocystis hominis was the most frequent parasite in HIV positive and negative patients. Being hospitalized and HIV infection were risk factors for coccidian infection, but age ≥ 40 years was a protective factor.