The objective of this work is to investigate influence of non-conformities at implementing and application of quality management system according to requirements of ISO 9001:2000. Investigation is performed on authentic systems during practical implementation of quality management systems in organizations. Requirements of quality management system according to ISO 9001:2000 are described. These requirements are defined by provisions of the norm ISO 9001:2000. Notion of audit is explained. Audit is used to check fulfillment of requirements of the norm. Procedures for execution of audits used for the purpose of this investigation are defined. Types of audit categorization and requirements for auditors are presented, too. Investigation includes 25 Croatian companies, with different scopes of activity, number of employees and type of ownership. Quality management systems of these companies were monitored in detail for four years. Internal audit reports were collected from companies, and author himself performed external audits at companies that were included in this investigation. Non-conformities that were issued at audits are grouped according to requirements of norm ISO 9001:2000. This data are analyzed to determine influence of number of employees, type of activity and ownership to non-conformities at quality management systems. Statistical analysis techniques of Pareto analysis, contingency tests and Spearman correlation rank analysis are performed. Analysis of internal and external quality audits results was used to determine those quality management system requirements, that were dificult to implement. For each of those requirements, explanation of cause of non conformity is given. These findings will be very useful for those who are implementing requirements of norm ISO 9001:2000 in their organisations. Results show significant differences at implementation of quality management system requirements at private and state owned companies, and at smaller and big companies. Requirements of norm ISO 9001:2000 for which differences were found, are defined and explained. However, type of activity that is performed in audited organization is not significant for non-conformities of quality management system. Therefore, requirements of norm ISO 9001:2000 are applicable at all kind of organizations, regardless of the activity they perform.