Point-of-use household water desalination systems (HWDSs) are becoming popular in Iran because of the deterioration of drinking water. This study aimed to determine the microbial quality of output water from HWDSs in Qom, Iran by using the heterotrophic plate count (HPC) method. Samples of input and output water from 30 HWDSs were collected over a six-month period. Heterotrophic bacteria were tested using the pour plate technique. At the first sampling stage, the HPC level in 23% of samples exceeded the 500 CFU/ml threshold level. On average, for 50% of samples, the HPC level of input samples was 0–10 CFU/ml, for 42% it was 10–100 CFU/ml and for 8% it was 100–500 CFU/ml. For output samples, for 25%, the level of HPC was 0–10 CFU/ml, for 43% it was 10–100 CFU/ml, for 24% it was 100–500 CFU/ml and for 8% it exceeded 500 CFU/ml. For total coliforms the most probable number test was positive for the first and third stages of sampling (3% input samples). The comparison of the averages with national standard values shows that in some cases, the contamination of output water from HWDSs in the city of Qom has been above the standard values.