The objective assessment of the level of odour in on-site sanitation systems is required when evaluating emerging technology options and maintenance practices. The purpose of this study was to measure the concentrations of hydrogen sulphide and ammonia as surrogates of odour using a portable gas detector, and assess whether the concentrations of the compounds correlate with the perception of users of the facilities. The Aeroqual 500 portable gas detector with hydrogen sulphide and ammonia sensor heads was used to measure the concentrations of the compounds in 88 private and seven communal latrines sampled from a peri-urban community in Ghana. The odour perception of 189 and 165 users of private and communal latrines, respectively, was assessed on an ordinal scale. It was found that the concentrations of hydrogen sulphide and ammonia measured with the gas detector reflected the known variation of odour levels among different technology options and the perceptions of the latrine users. The concentrations of hydrogen sulphide measured in the water closet, ventilated improved pit (VIP) and the simple pit latrines were 0.01, 0.03 and 0.13 ppm, respectively; those of ammonia were undetected for the water closet, and 0.30 and 3.27 ppm for the VIP and simple pit latrines, respectively. The Pearson correlation coefficient between hydrogen sulphide concentrations and user perception of odour (−0.234) was significant at 5 % level (p = 0.022) but that for ammonia was not. The results indicate that a portable hydrogen sulphide detector may be employed to objectively assess the effectiveness of new latrine designs and maintenance practices aimed at reducing odour in latrines.