Objectives Malnutrition is an unfavorable prognostic factor associated with an increase in mortality, hospital stays, readmissions and resources consumption. The aim was to screen primary care patients for risk of malnutrition by using the control nutritional (CONUT) score, calculated through total lymphocytes count, serum albumin and total cholesterol, when the three markers were requested, and to compare results between primary care centers (PCC). Methods The clinical laboratory located in a 370-bed suburban University Community Hospital serves the Health Department inhabitants (2,34,551), attended in nine PCC. The laboratory information system (LIS) automatically calculated the CONUT score in every primary care patient over 18 years old, when all three laboratory markers were ordered by the General Practitioner. For all primary care patients, we collected demographic data, CONUT index and PCC. We classified results by PCC, and compared them. Results The clinical laboratory received 74,743 requests from primary care. The CONUT score was calculated in 7,155 (12.28%) patients. Nine hundred seventy-six (13.6%) were at risk of malnutrition according to the CONUT score, mainly male (p<0.01) and over 65 (p<0.01). Detected cases of malnutrition were all mild, except 48 patients (4.9%) with moderate, and one (0.1%) with severe risk. The percentage of patients at risk of malnutrition was not significantly different among PCC, with the exception of one with patients at lower malnutrition risk. Conclusions It is possible to use CONUT score as a front-line population-wide laboratory marker to screen for the risk for malnutrition in primary care patients that was lower in one PCC.