Cholera was first detected in Papua New Guinea in July 2009, caused by Vibrio cholerae O1 El Tor serotype Ogawa. By late 2011, 15 500 cases had been reported throughout lowland Papua New Guinea with a case fatality rate of 3.2%. The epidemic has since slowed, with only sporadic cases reported in Western Province and the Autonomous Region of Bougainville (ARB). Accurate and timely diagnosis is a critical element of the public health response to cholera, yet in low-income countries where the burden of cholera is the greatest, diagnostic services are often limited. Here we report on the diagnostic challenges and the logistical factors that impacted on diagnosis during the first reported outbreak of cholera in Papua New Guinea.