Diarrhoeal disease is one of the leading causes of mortality and morbidity globally. Non-biting synanthropic flies are of public health importance due to their habit of flying between faecal matter and households, potentially transmitting pathogenic bacteria by regurgitation, defecation or mechanical transmission via legs or wings. Lymphatic filariasis (LF), caused by Wuchereria bancofti and transmitted by Culex quinquefasciatus, affects approximately 120 million people in Asia. Controlling the mosquito vector can have a significant impact on LF incidence rates. It is assumed that increasing the coverage of latrines will reduce the amount of open defecation and environmental faecal contamination resulting in a healthier population. However, few studies have measured the impact of building latrines on human health and even fewer have demonstrated its impact on synanthropic fly populations or their bacterial carriage and associated diarrhoeal disease. Similarly, although Cx. quinquefasciatus has long been associated with pit latrines, the resulting impact through the construction of improved pour-flush latrines on population densities has yet to be explored. Initial experiments were conducted to determine the best methodology for trapping both synanthropic flies and Cx. quinquefasciatus, to inform the design of the entomological component of a cluster randomised control trial (cRCT). Thereafter, the focus was on determining the impact of latrine construction on the exposure of households to populations of flies and the bacteria that they carry, and on Cx. quinquefasciatus densities and W. bancofti prevalence. Results indicate that latrine construction had no impact on the density of flies within households or on the carriage of bacteria. There was no statistical difference between control and intervention arms in the population density of synanthropic flies (IRR=0.89; 95%CI=[0.76-1.03]; p=0.131). There was a significant correlation between fly numbers and rainfall. Data were analysed by season for between arm differences; in the monsoon season 40% fewer flies were caught in the intervention arm compared to the control arm (p=<0.001). Most flies caught belonged to the Muscidae family: Musca domestica or M. sorbens. Of the flies tested for bacteria, 60.3% were positive for at least one of either Escherichia coli 0157:H7, Vibrio cholerae, Salmonella spp. or Shigella spp.. Escherichia coli was detected most frequently with 46% testing positive. Numbers of Cx. quinquefasciatus caught (IRR=0.88; 95%CI=[0.74-1.06]; p=0.178). between the control and intervention villages. Less than 1% of Cx. quinquefasciatus tested positive for W. bancrofti, equivalent to an LF prevalence rate of 0.0034% within the vector population. Latrine construction was not associated with a reduction in the densities of vectors and their pathogens, compared to villages without latrines. However, it should not be concluded that latrines have little value in improving public health. Reducing open defecation is one step towards limiting fly population densities and bacterial contamination in the environment, by reducing available larval habitats. However, latrine coverage by itself is not enough to prevent open defecation; construction needs to be supported by behaviour change. These findings reflect that there are multiple pathways for the spread of bacteria in the environment, one of which is fly-borne. In environments with high bacterial transmission reducing fly numbers alone is not enough to impact the transmission of diarrhoeal pathogens.