The aim of this study was to investigate effects of unplanned pregnancy on neonatal health. This is a retrospective case–control study and included 314 babies selected with a non-probability method. Data were collected with a questionnaire of descriptive characteristics and neonatal health and Parent Infant Interaction Assessment Scale. A significantly higher rate of the babies born to the women with unplanned pregnancy had meconium in their amniotic fluid (14.6% vs. 7.0%; P = 0.029), needed special care (20.4% vs. 11.5%; P = 0.031) and were kept in the incubators (12.7% vs. 4.5%; P = 0.009). Both the babies born to the women with unplanned pregnancy and the babies born to the women with planned pregnancy were first fed with breast milk (96.8% of the unplanned group; 98.1% of the planned group), but a higher rate of the babies born to the women with unplanned pregnancy had problems with breast-feeding. (19.1% vs. 5.1%; P = 0.000). The babies born to the women with unplanned pregnancy got significantly lower scores on Parent Infant Interaction Assessment Scale (4.86 ± 1.98 in the unplanned group; 8.52 ± 1.43 in the planned group; P = 0.000). We found that a higher rate of the babies born to the women with unplanned pregnancy needed special care, had problems with breast-feeding and negative parent–infant interaction. We recommend that women with unplanned pregnancy should be given priority on prenatal, intrapartum and postpartum care and that measures which protect and promote neonatal health should be taken.