This study was conducted to investigate the factors that affect performance of students in sciences using HASASS, Jega as the case study .The study adopted the use of questionnaires and observation schedule as the instruments in collecting data. The mean and percentage were used to analyze the data obtained. The results revealed that the performance of students in sciences during previous SSCE/NECO and internal examinations was unsatisfactory. Factors identified as responsible for unsatisfactory performance included inadequate professionally qualified science teachers, non existence of laboratory personnel, inadequate laboratory equipment and instructional materials.Recommendations on ways to improve the students performance to a high level of achievement were therefore made.