The aim of this study is to identify cell-related misconceptions among fifth graders attending middle schools in Turkey and examine the impact of microscopy on the elimination of these misconceptions. The study was conducted with the participation of 87 fifth grade students (schoolchildren are nearly 11 years old) attending a middle school in Agri province of Turkey in the academic year 2015-2016. The research was designed as a case study and data were collected using a test with 4 diagnostic and drawing items. Data analysis showed that the students had cell-related misconceptions. Prior to instruction with a microscope, most students thought an onion cell was shaped like an onion and it was a cooking ingredient their mothers used. They said that a leaf cell was shaped like a leaf and described it as a leaf on a tree. They described bacteria as living things with organs and limbs, like animals. They drew and described bread mold as a loaf of bread. Most of these misconceptions were found to disappear after learning with a microscope.