Children’s knowledge about human anatomy can be examined through several different ways. Making a drawing of the internal features of the human body has been frequently used in recent studies. However, there might be a serious difference in results obtained from a general instruction to students (What you think is inside your body) and specific (e.g. Draw bones that are inside your body) instruction. We examined relationships between these two types of instructions using drawings of the urinary and endocrine systems as the examples with pupils aged 10-14 years. An ANCOVA showed significant relationships between general and special instruction, but further comparison showed significant correlation only for urinary system. The level of students’ drawings significantly increases with previous knowledge about human anatomy and age. These findings suggest that relationships between two types of instructions strongly depend on the complexity of the organ system that children draw as well as their previous knowledge. We propose that drawings from general instructions are therefore appropriate especially for comparative studies. Special instructions are better for eliciting a deeper understanding of children knowledge about human anatomy.