The most common and polite way to say "How are you?" in Japanese is: お元気ですか？ (Ogenki desu ka?) This phrase literally means "Are you well?" or "Are you energetic?" and is widely used in both formal and semi-formal settings to ask about someone's well-being.

For less formal or casual contexts, you might simply say: 元気？ (Genki?) which also means "How are you?" but in a more casual and friendly tone.

Thus, "How are you?" in Japanese is commonly expressed as お元気ですか？ (Ogenki desu ka?) in polite speech and 元気？ (Genki?) in informal speech.