The footprint of human activities within Antarctica is increasing, making it essential to consider whether current conservation/protection of environmental and scientific values is adequate. The Antarctic protected area network has developed largely without any clear strategy, despite scientific attempts to promote protection of representative habitats. Many Antarctic Specially Protected Area (ASPA) Management Plans do not state clearly if conservation or science is the priority objective. This is problematic as science and conservation may have conflicting management requirements, i.e. visitation may benefit science, but harm conservation values. We examined recent estimated mean annual levels of visitation to ASPAs. On average, ASPAs protecting scientific research interests were visited twice as often as ASPAs conserving Antarctic habitat and biological communities. However, ASPAs protecting both science and conserving habitat were visited three times as often as ASPAs conserving habitat alone. Examination of visitation data showed that the proportion of visitors entering ASPAs for science, environmental management and/or education and tourism purposes, did not reflect the primary reason for designation, i.e. for science and/or conservation. One third of APSAs designated since the Environmental Protocol entered into force (1998) did not describe clearly the main reason for designation. Policy makers should consider (i) for all Management Plans stating unambiguously the reason an area has ASPA designation, e.g. either to protect habitat/environmental values or scientific research, in accordance with adopted guidance, (ii) designating new protected areas where visitation is kept to an absolute minimum to ensure the long-term conservation of Antarctic species and habitats without local human impacts (possibly located far from areas of human activity), and (iii) encouraging the use of zoning in ASPAs to help facilitate the current and future requirements of different scientific disciplines.