In October 2013, the Radiation Medical Science Center of the Fukushima Medical University and the Section of Environment and Radiation of the International Agency for Research on Cancer held a joint workshop in Fukushima, Japan to discuss opportunities and challenges for long-term studies of the health effects following the March 2011 Fukushima Daiichi Nuclear Power Plant Accident. This report describes four key areas of discussion -- thyroid screening, dosimetry, mental health, and non-radiation risk factors -- and summarizes recommendations resulting from the workshop. Four recommendations given at the workshop were to: 1) build-up a population-based cancer registry for long-term monitoring of the cancer burden in the prefecture; 2) enable future linkage of data from the various independent activities, particularly those related to dose reconstruction and health status ascertainment; 3) establish long-term observational studies with repeated measurements of lifestyle and behavioural factors to disentangle radiation and non-radiation factors; and 4) implement primary prevention strategies targeted for populations affected by natural disasters, including measures to better understand and address health risk concerns in the affected population. The workshop concluded that coordinated data collection between researchers from different institutes and disciplines can both reduce the burden on the population and facilitate efforts to examine the inter-relationships between the many factors at play.