Morocco is undergoing nutrition transition with more than one third of women and children presenting anaemia while about 20% of children under the age of 15 years have stunted growth. Meanwhile the prevalence of obesity is increasing yearly by 0.5 to 1 point among women. Many nutritional strategies have been proposed but none has been implemented. Nutrition education and food based strategies are by far the most sustainable. Dietary diversity is used for the assessment of diet quality and food security. Morocco is still suffering from a heavy burden of many micronutrient deficiencies and child stunting. The purpose of the study was to assess dietary diversity by comparing a dietary diversity score (DDS) and a weekly food frequency score (WFFS) and study their relationship to anaemia and stunting in school-age children in the province of Kenitra (Morocco). A stratified random sample of 263 pupils with average age of 12.9 ± 0.9 years including one-third from rural schools were administered a weekly food frequency questionnaire. A health team assessed the anthropometric status and blood haemoglobin levels. Dietary diversity was appraised with two types of indices: a dietary diversity score (DDS) based on the number of food categories consumed over a week, and a weekly food frequency score (WFFS) which also takes into account the frequency of food intake. The DDS was significantly higher in rural than in urban children, whereas the WFFS was lower, in rural children owing primarily to less frequent intake of fruits and vegetables than in the urban children. Maternal level of instruction was also positively associated with a higher consumption of fruits and vegetables and milk, and with a higher WFFS. Both indices were significantly associated with stunting but not with anaemia. In conclusion, these results suggest that diet quality is associated with height status and food diversity indices that take food frequency into account may provide a better reflection of diet quality.