This descriptive research was done on atomic structure and periodic table topics in SMAN 7 Padang. On these topics, students had difficulties on achieving learning goals where only 38% students could achieve the minimum defined criteria. This research aims to determine percentage of learning difficulties in all learning indicators and find factors that cause learning difficulties. 57 tenth grade students as research sample were obtained through cluster sampling technique. Research instruments used were diagnostic test and questionnaire and data were then analyzed descriptively. Analysis showed that learning difficulties were 91.2%, 13.2%, 88.3%, 51.5%, 70%, 64%, 84%, 84%, and 74.9% in the indicator of describing subatomic particles and their discovery; determining atomic number and mass number of elements and isotopes; describing atomic model according to Dalton, Thomson, Rutherford, Bohr, and wave mechanics; explaining electron configuration and orbital diagrams; determining quantum number and orbital shape; describing development of periodic system; modern periodic system; periods and groups in periodic table; and periodic trends of elements respectively. Students’ learning difficulties were influenced by school factors including teaching methods 35.8%, curriculum 47.5%, teacher relation with students 49.1 %, relation among students 41.7%, time and school discipline 33.3%, teaching tools 39.4% and school building condition 17.7%.