Eighty-six varicella-zoster virus (VZV) strains of clades 1, 3 and 5, isolated from varicella and zoster patients in Germany, were analyzed by sequencing the glycoprotein E gene. Four novel non-synonymous and 10 novel synonymous mutations were detected. Of these, two synonymous (C513T, C885T) and two non-synonymous mutations (T485G, C524T) were located within the coding regions of e1 and c1. The profile of single-nucleotide polymorphisms was found to be significantly associated with the VZV clades 1, 3 and 5.