Background Low folate and vitamin B12 concentrations during pregnancy are implicated with neural tube defects (NTD) and neurological manifestations in the neonates. Aim To compare serum concentrations of folate and vitamin B12 in 1025 Greek mothers, 908 immigrant Albanian mothers at delivery and in the cord blood of their neonates. Methods A 30 days food diary was kept from each mother. Folate and vitamin B12 sera concentrations were measured with Bayer ADVIA Centaur System. Results Energy, carbohydrates and total fat intake were significantly higher in Albanian mothers when compared with those of Greek origin. On the contrary, total protein, and especially animal protein intake were higher in the Greek mothers. Folate intake was similar between the two ethnic groups whereas vitamin B12 intake in Albanians was evaluated lower (1.8 ± 0.13 μg day−1) when compared with that of Greeks (2.8 ± 0.12 μg day−1; P < 0.001). Folate serum concentrations in mothers and newborns were similar (17.7 ± 9.1 and 26.5 ± 15.2 nm versus 18.1 ± 8.6 and 24.6 ± 14.7 nm, respectively P > 0.05) in the two ethnic groups. In contrast, vitamin B12 serum concentration was significantly lower (135.0 ± 19.6 pm) in the Albanian mothers compared with that of Greeks (164.5 ± 17.7 pm, P < 0.0001). Consequently, the vitamin concentrations was found lower in the newborns of Albanian origin (133.6 ± 11.8 pm) compared with that of Greek neonates (213.3 ± 11.4 pm, P < 0.0001). Conclusions (a) Folate serum concentrations in Greek and Albanian mothers and in their neonates were similar, (b) vitamin B12 serum concentrations, evaluated for first time in these ethnic groups, were significantly low in Albanians, both in mothers and newborns, (c) the low protein and especially the reduced animal protein intake from the Albanian mothers, possibly due to their low socio-economic status, may be responsible for their decreased vitamin B12 serum concentrations and (d) vitamin B12 supplementation along with an increase of animal protein intake might improve the vitamin serum status in the Albanians.