Research developments in the contemporary market economy shows that the chances of market dominance to entities specializing in the provision of specific services to meet the needs and preferences of customers. Actors such transportation are the organizers who are able to assume responsibility for the functioning of certain segments of the public transport market. Under certain conditions, system, now dominant, transport organizers occupy a monopoly position around which creates a team of support units, and in this respect the stakeholders. One group of stakeholders close, surgically shaped public transport market can be and are non-governmental organizations. The effectiveness of a particular NGO, as a stakeholder, personal preference - realized in the structure of public transport - it depends of course on the possible effects on the organizer. This ability is in turn a function of the economic health of the organization, which is, however, a multifactorial category. To objective this process must be concluded that it is possible to create and use the system's potential for diagnosing The practice of NGOs indicates that the most important metrics associated with the assessment of their performance indicators related to the financial balance of revenue and expenditure. Also streamline diagnosis to assess their solvency and liquidity. Together they determine not only the ability to take short-term action, but also provide opportunities to continue in the future. Diagnostic measures to evaluate the effectiveness of non-governmental organizations should also include those that are related to the probability of obtaining external funding support, in specific cases related to their debt. Are also important non-financial measures, the organization's environment, and in this respect: the number of people using transport services organized by the governmental unit, the number of effective interventions made by the organization in matters of special needs transport service or a trend in the development of the invoiced value of social services. These measures define only the basic attributes of a diagnostic system design universally grasped NGO. Detailed studies of the specific activities of various non-governmental organizations will allow for a comparative analysis of their activity and thus, to improve the precision of the projection system diagnostic assessment of each such entity. active non-governmental organizations, to evaluate the ability to shaping the market and public transport by these units. Any diagnosis of the organization is based on theoretical assumptions that allow us to study how effectively the organization operates, which are the dominant sub-goals, which may be the source of failure or success conditions. Consequently, it can be assumed that NGOs diagnostic system will consist of a number of diversified measures highlighted features of assessment, however, often goes beyond the commonly used measure of management efficiency.