Background: The rate of twinning continues to increase due to the combined effect of a rise in parental age and increased use of assisted reproductive technology. The risk of congenital anomalies in twins is higher than in singletons, but it is less well reported in relation to growth patterns. We focused to the auxological outcome of twin pregnancies when one or both of twins are affected by one or more malformations. Methods: We conducted a retrospective observational study reviewing the clinical charts of twins admitted in the period between January 2003 and December 2018 at the University Hospital of Palermo. The associations between malformations and anthropometric variables at birth were analyzed by comparison within each twin pair and regarding each variable as ordered difference between the two twins. Results: We studied data of 488 neonates (52% females) from 244 pregnancies. The rate of major congenital anomalies was 11%, affecting significantly the smaller twin (p = .00018; Odds ratio 3.21; 95% CI 1.65 6.59). Malformation class distribution was as following: genitourinary (24%), gastrointestinal (20%), cardiovascular (18.5%), musculoskeletal (11%), central nervous system (9%), syndromic (9%), ocular (5.5%) and diaphragmatic hernia (2%). The most predictive value, the Birthweight (BW) difference mean ratio in malformed versus not malformed neonates (− 0.31 vs 0.02; p = .0016) was distributed equally lower than zero in all malformed twins, except for those with congenital heart defects (p = .0000083). Microcephaly (head circumference < 2 standard deviation, SD) was present in 3% of symmetrically smaller twin, and severe microcephaly (< 3 SD) was present in 0.6%. We found that an intertwin BW discordance of 18% or greater identified 50% of neonates with microcephaly, but only 11% of malformed twins. Conclusions: In case of one twin with a BW < 10th centile, a concomitant intertwin BW discordance ≥18% could reveal an increased risk for microcephaly but not for malformation. Lower values of BW, Ponderal index, Body mass index but above all negative value of BW difference mean ratio are associated with malformations in twin pairs.