The spinocerebellar ataxias (SCAs) with autosomal dominant inheritance are a clinically and genetically heterogeneous group of neurological disorders with overlapping as well as highly variable phenotypes primarily affecting the cerebellum. To date, 28 different loci have been identified. Nine SCAs are caused by repeat expansions; for 14 only the chromosomal localisation is known. Recently, two frameshift mutations in the tau tubulin kinase 2 gene (TTBK2) were reported to cause SCA11. To evaluate the frequency of mutations in the TTBK2 gene, we performed molecular genetic analyses in 49 unrelated familial cases with ataxia. Sequencing all coding exons revealed, amongst others, two novel missense exchanges at evolutionarily conserved amino acid positions. Although being unique in 98 alleles of ataxia patients, a disease causing effect can be excluded with high probability for both variations. This result demonstrates the challenges in diagnostic testing for SCA11.