BACKGROUND: Investigate the role of latent strongyloidiasis infection in patients at the University Hospital, Honduras. METHODS: Prospective observational cohort study during 20 non consecutive months from March 2009 to February 2011. Epidemiological and clinical data obtained from patients excreting Strongyloides stercoralis larvae in stool who consulted at the hospital were recorded and analyzed. RESULTS: Thirty five (5 %) of 712 patients had S. stercoralis larvae in one stool sample; 62.8 % came from rural areas and 91.7 % were poor; 68.5 % (24/35) were 21 years old or older. Eight patients (22.8 %) had no predisposing illness; 3 (8.6 %) received steroid treatment, 29/35 (82.8 %) presented with persistent diarrhea and 24/35 (68.5 %) presented following comorbidities: HIV/AIDS (31.4 %), alcoholism alone (11.4 %) or with other associated illness (8.6 %), malignancy (8.6 %), renal failure (5.7 %) and hyperthyroidism (2.8 %). A combination of symptoms suggestive of strongyloidiasis but indistinguishable from those potentially associated to their comorbid condition included severe epigastric pain, diarrhea of weeks duration, peripheral eosinophilia, astenia, adynamia, fever, anemia and weight loss in 85.7 % of the cases, 3 of whom described skin lesions compatible with larva currens. None of the diagnostic clinical impressions mentioned Strongyloides infection. Ten strongyloidiasis patients received partial treatment with albendazole or ivermectin. Incomplete data, underestimation of the parasitic infection and no laboratory follow-up of the patients limited our observations. CONCLUSIONS: Strongyloides stercoralis is an unsuspected and neglected parasitic infection by health personnel in Honduras. Lack of awareness of its importance represents a strong barrier to proper treatment and follow-up, posing a threat of possible fatal complications in patients with comorbid conditions.