Secondary school students face many difficulties to understand the lessons of the biology course. These difficulties may be related to the topics of the biology course, to the way teacher explains, his style, the way he introduces the topics, and his use of modern methods to help understanding topics. School environment may cause distraction, lack of concentration, or inability to follow up on understanding lessons. The current research aimed to study the various difficulties faced by the male students of Al-Nokrashy Secondary School in Hadyek El Koba administration, by conducting personal interviews and applying questionnaires, the results of which were that the students stated that the most difficulties facing them in studying and understanding the biology course are related to the topics of the biology course itself with percentage of (54%), followed by the teacher (47.6%) and finally the difficulties related to the school environment (32.2%). At the end of the research, the researchers supposed solutions that would handle the difficulties faced by students at Al-Nokrashy Secondary School, in particular, and could be applicable to all secondary schools in general to improve necessary skills of secondary school students to understand biology course smoothly and easy.