This study provides an in-depth investigation of Turkish trainee teachers perceptions of the greenhouse effect. The sample of the research is composed of total 218 elementary level trainee teachers at Uludag University in Turkey, in 2014. Within the targeted group of respondents, 35.3% were at Science Education, 32.6% at Primary Education and 32.1% at Social Studies Education Department. Besides, this study aimed to investigate the influence of gender and being at different departments on trainee teachers perceptions regarding of the greenhouse effect. It was used the Environmental Issues Questionnaire during data collection process. There is a statistically significant difference between girls and boys and the average of boys is higher than the average of girls. One-Way Anova test results show that there is not a statistically significant difference between groups. Based on the findings, it can be concluded that many trainee teachers have several misconceptions concerning the greenhouse effect. Many aspects of the greenhouse effect are still confusing for them. It is thought that the complexity of environmental problems leads to elementary trainee teachers many misconceptions.