Background: Childhood obesity is a growing concern in Sweden. Children with overweight and obesity run a high risk of becoming obese as adults, and are likely to develop comorbidities. Despite the immense demand, there is still a lack of evidence-based comprehensive prevention programmes targeting pre-school children and their families in primary health care settings. The aims are to describe the design and methodology of the PRIMROSE cluster-randomised controlled trial, assess the relative validity of a food frequency questionnaire, and describe the baseline characteristics of the eligible young children and their mothers. Methods/Design: The PRIMROSE trial targets first-time parents and their children at Swedish child health centres (CHC) in eight counties in Sweden. Randomisation is conducted at the CHC unit level. CHC nurses employed at the participating CHC received training in carrying out the intervention alongside their provision of regular services. The intervention programme, starting when the child is 8-9 months of age and ending at age 4, is based on social cognitive theory and employs motivational interviewing. Primary outcomes are children's body mass index and waist circumference at four years. Secondary outcomes are children's and mothers' eating habits (assessed by a food frequency questionnaire), and children's and mothers' physical activity (measured by accelerometer and a validated questionnaire), and mothers' body mass index and waist circumference. Discussion: The on-going population-based PRIMROSE trial, which targets childhood obesity, is embedded in the regular national (routine) preventive child health services that are available free-of-charge to all young families in Sweden. Of the participants (n = 1369), 489 intervention and 550 control mothers (75.9%) responded to the validated physical activity and food frequency questionnaire at baseline (i.e., before the first intervention session, or, for children in the control group, before they reached 10 months of age). The food frequency questionnaire showed acceptable relative validity when compared with an 8-day food diary. We are not aware of any previous RCT, concerned with the primary prevention of childhood obesity through sessions at CHC that addresses healthy eating habits and physical activity in the context of a routine child health services programme.