Meconium ileus (MI) is a risk factor for poor outcomes in cystic fibrosis (CF) patients. The aim of this study was to identify the risk factors for poor 12-month clinical outcomes in MI-CF newborns. This retrospective, multicentre, observational study of MI-CF infants born 2009-2015 recorded their pre- and neonatal histories, intestinal occlusion treatments, post-surgical history, nutrition, CF diagnosis, and compared the patients with 12-month faltering growth or chronic Pseudomonas aeruginosa respiratory infection (cases) with the others (controls). About 25% of the 85 patients enrolled by 13 Italian CF centres (24% premature, 18% of low birth weight) had prenatally diagnosed bowel obstruction, and 39% had complex MI. Seventy-one required surgery (the 33 with complex MI and 38 with simple MI), of whom 58 (82%) required post-surgical intensive care, including 25 (35%) needing ventilatory support. Forty-six (54%) were breastfed; exclusively parenteral nutrition was started in 52 (61%). Cholestasis was diagnosed in 21%. Thirty-one (37%) experienced negative outcomes: the only risk factors were prenatally diagnosed intestinal obstruction and a need for intensive care and oxygen therapy. The cases had significantly higher first blood immunoreactive trypsinogen (b-IRT) levels (P = .008). Logistic regression showed that the probability of having negative outcome is decreased in the absence of cholestasis (Odds Ratio = 0.125) and a need for intensive therapy (OR = 0.141), and increased by not having been breastfed (OR = 2.921). High b-IRT levels, prenatally diagnosed intestinal obstruction, a severe post-surgical clinical picture and early liver disease are risk factors for negative outcomes. Breastfeeding may be protective. Copyright © 2019. Published by Elsevier B.V.