Twenty infectious bronchitis virus isolates were recovered from broilers and layers in different outbreaks amongst commercial poultry flocks in different geographic regions of Argentina from 2001 to 2008. The viruses were isolated from the tracheas, lungs, and caecal tonsils of birds that were showing respiratory signs. Further analysis based on their nucleotide and amino acid sequences in hypervariable region (HVR) 1 and the intervening sequence including HVRs 1 and 2 (HVR1/2) of the S1 gene was done to determine the genetic relationships among them and reference strains. Five isolates were highly related to the Massachusetts or Connecticut serotypes, indicating the probability of the detection and isolation of vaccine strains. The other Argentinean isolates formed three separate clusters (A, B and C), distant from the vaccine serotypes, with no correlation between the generated clusters and a geographic pattern. These observations could explain the failure of the Massachusetts serotype vaccination programmes to control IBV in these flocks. In addition, the utilization of HVR1/2 and HVR1 sequences resulted in trees with similar topology but the phylogenetic relationships using HVR1/2 nucleotide sequences were better supported by higher bootstrap values. Therefore, the sequences of the HVR1/2 region are recommended for phylogenetic studies.