The congenital disorder of glycosylation (CDG)-Ic (ALG6-CDG, CDG-Ic) is caused by mutations in the hALG6 gene that encodes the N-glycosylation pathway enzyme, α-1,3-glucosyltransferase (NP_037471.2). The aim of our study was to estimate the frequencies of ALG6-CDG related p.Y131H and p.F304S polymorphisms in the Croatian population. Genomic DNA was isolated from blood samples collected from 600 healthy individuals. Functional single-nucleotide polymorphisms rs35383149 and rs17856039 causing p.Y131H and p.F304S, respectively, were genotyped by the TaqMan method and direct sequencing. The frequency of p.F304S polymorphism in the studied cohort was shown to be similar to the frequencies found in other tested populations (27%), whereas the frequency of p.Y131H was found to be three times higher (6.7%). Five novel base substitutions in the hALG6 gene were also found: three in exon 5 (c.383T>C, c.390G>A, and c.429G>C) and two in a downstream intervening sequence (IVS5+17C/T and IVS5+34G/A).