<h3>Background</h3> The lethal short rib polydactyly syndromes (SRP type I–IV) are characterised by notably short ribs, short limbs, polydactyly, multiple anomalies of major organs, and autosomal recessive mode of inheritance. Among them, SRP type II (Majewski; MIM 263520) is characterised by short ovoid tibiae or tibial agenesis and is radiographically closely related to SRP type IV (Beemer-Langer; MIM 269860) which is distinguished by bowed radii and ulnae and relatively well tubulated tibiae. <i>NEK1</i> mutations have been recently identified in SRP type II. Double heterozygosity for mutations in both <i>NEK1</i> and <i>DYNC2H1</i> in one SRP type II case supported possible digenic diallelic inheritance. <h3>Methods</h3> The aim of this study was to screen <i>DYNC2H1</i> and <i>NEK1</i> in 13 SRP type II cases and seven SRP type IV cases. It was not possible to screen <i>DYNC2H1</i> in two patients due to insufficient amount of DNA. <h3>Results</h3> The study identified homozygous <i>NEK1</i> mutations in 5/13 SRP type II and compound heterozygous <i>DYNC2H1</i> mutations in 4/12 cases. Finally, <i>NEK1</i> and <i>DYNC2H1</i> were excluded in 3/12 SRP type II and in all SRP type IV cases. The main difference between the mutation positive SRP type II group and the mutation negative SRP type II group was the presence of holoprosencephaly and polymycrogyria in the mutation negative group. <h3>Conclusion</h3> This study confirms that <i>NEK</i>1 is one gene causing SRP type II but also reports mutations in <i>DYNC2H1</i>, expanding the phenotypic spectrum of <i>DYNC2H1</i> mutations. The exclusion of <i>NEK1</i> and <i>DYNC2H1</i> in 3/12 SRP type II and in all SRP type IV cases further support genetic heterogeneity.