The first nationwide study on a patient referral system was conducted in Honduras. It covered all 25 public hospitals (six National, five Regional and 14 Area Hospitals) and 24 major health centres. Based on 46 739 reviews of patient records, 226 ‘received referral’ and 1072 ‘sent referral’ cases were analyzed by age and sex of the patient, diagnosis on referral, institution from or to which the case was referred, use of proper referral form, and reception of reply for referrals. At the same time, the study team supervised the function of the registry and management of patient records at each institution. The average referral rate by the level of health facility was 15.8% at National, 4.0% at Regional, 2.8 % at Area Hospitals, and 0.8 % at health centres. The referral rate was observed to be higher when institutional managers emphasized the importance of the referral system. Only 1.4% of referrals received a reply from upper level institutions. The most common cases for referral were neurological at National, obstetric at Regional and respiratory cases at Area Hospitals. The use rate of the standard referral form was 70 to 80 % at hospitals and 60 % at health centres. There was no norm to duplicate referral letters for record keeping. The patient referral system has not developed satisfactorily in Honduras. The main problems were: 1) low referral rate at all levels of institution, 2) evident by-pass phenomenon at intermediate hospitals, 3) inadequate health information system for patient referral, and 4) misunderstanding of the terminology of referral by health personnel. The following recommendations were made: guarantee of essential health services at peripheral institutions, development of an effective information system for patient referral, facilitation of frequent reply for referrals, elaboration of referral case discussion between institutions, patient education on proper use of health facilities, and restructuring the health service network in the two major cities.