Objective: To evaluate factors present on newborn admission to a neonatal intensive care and associated with a prolonged hospital stay. Patients and Method: Non-matched case-control study, with 555 infants, 111 with more than 7 days of hospital stay and 444 who stayed hospitalized between 1 and 7 days, between 2005 and 2010. Pre hospitalization maternal factors (age, pregnancy, health insurance, education, prenatal care, marital status, history of preeclampsia, prolonged rupture of membranes, chorioamnionitis infection) and neonatal ones (age at admission, gestational age, birth weight, gender, delivery practice, route of admission, Apgar and type of resuscitation) that were associated with prolonged hospital stay were analyzed. Analyses were conducted using STATA 11.0 and logistic regression in the multivariate analysis. Results: Maternal factors such as prenatal care with less than 5 doctor visits (AOR 2.7, 95% CI 1.3-5.5), lack of social health insurance (AOR 1.9, 95% CI 1.4-29), pregnant three or more times (AOR 1.7, 95% CI 1.1-2.7), neonatal birth weight under 2,000 g (AOR 4.2, 95% CI 1.9-9.5), need for cardiopulmonary resuscitation (AOR 4.2, 95% CI 2-9.1), gestational age less than 36 weeks (AOR 3.9, 95% CI 2-7.7) and admission to the neonatal unit through emergency room or referral from another hospital (AOR 2.8, 95% CI 1.7-4.6) were associated with hospital stays longer than 7 days. Conclusions: In-hospital complications that affect a prolonged stay at the health center were social health insurance, maternal education and prenatal care, and these should be considered in the evaluation of the hospital care quality indicators.