The aim of this study was to assess the perceptions of Ph.D. candidates and supervisors regarding how well Ph.D. students fulfill the learning outcomes specified for third-cycle higher education in Sweden. Data were gathered using a survey sent to doctoral students and supervisors at five departments at Lund University and one department at Malmö University. The investigation concentrated on 18 skills outlined in the learning objectives and on specific analyses of student and supervisor ratings, gender differences, and differences across departments. Responses from 123 survey participants show that skills for specialized knowledge and specific method competencies were rated most highly by respondents, while skills relating to contributing to others’ learning, ethics, presenting to society, and identifying limitations of research were rated lower than average. In 14 of the 18 skills, supervisors rated the students’ competencies higher than the students rated themselves. Although the highest-rated skills were rated similarly by male and female respondents, there were gender differences for other learning objectives (e.g., ethics, personal knowledge, and autonomy). Responses from the Biology and Physics departments revealed differences in both how students and supervisors rate Ph.D. candidate performance and certain individual learning objective skills. Our results demonstrate large differences in the appraisal of learning outcomes in individual cases by students and supervisors, and that these assessments can be influenced by gender and academic culture. For the third-cycle learning outcomes to actually promote student learning and be a useful tool for quality assurance, supervisors and students must be aware of their existence, and care must be given to apply and assess the generic learning objectives in the context of particular disciplines, with the consideration of the specific needs of individual doctoral students. Embedding the learning outcomes in individual Ph.D. study plans would be a good initial step to meet this goal.