Vitamin D3 50,000 IU is a convenient high dose capsule that only needs to be taken once a week. It provides an immediate boost and is best for anyone who has trouble reaching and maintaining peak vitamin D levels. Generally, this capsule is not recommended for long-term daily use. By contrast, Vitamin D3 5,000 IU is a smaller dose that is taken more frequently (typically daily). Some of it comes down to personal preference in terms of how often you want to take the supplement.