BACKGROUND: The Healthy Eating Active Living TeleHealth Community of Practice is a virtual quality-improvement learning network of seven rural clinics in California. The goal of this network is to improve childhood obesity prevention and management practices at participating clinics. AIM: Our objective is to describe clinical practices regarding weight assessment and nutrition and physical activity counselling at participating clinics before implementation of the quality improvement intervention. METHODS: Participants were 2–11 year old children seen for well-child care in 2010. Telephone surveys of English and Spanish-speaking parents were conducted within three days of their child’s well-child visit to determine the content of counselling during the visit regarding nutrition and physical activity. Medical record reviews were conducted to determine clinicians’ assessment of weight status. FINDINGS: Twenty-seven clinicians conducted 144 well-child visits included in the study. Body mass index (BMI) was documented in 71% of medical records. Fewer than 10% of medical records had documentation of weight category. Sixty-nine percent of parents received counselling on physical activity and 62% reported receiving counselling on fruit and vegetable intake. Parents were counselled less frequently on breakfast intake, sweetened beverages, television and family meals. Parents of overweight/obese children did not receive more counselling than parents of children with a healthy BMI. Clinician-level effects accounted for moderately large amount of variation in counselling, but accounted for smaller variation in documentation of BMI and weight category. There was high between-clinic variation in documentation practices, with 54% of the total variance for documentation attributable to clinic-level effects. CONCLUSIONS: Rural clinicians, like those elsewhere, do not uniformly assess BMI percentile or counsel families on behavioural risk factors for paediatric obesity. There exists considerable clinician-level variation in counselling practices and clinic-site level correlation in documentation practices related to BMI percentile and weight category.