I have been to Japan.我去過日本。例如："How many countries have you visited?（你去過幾個國家?）" "I have only been to Japan（我只去過日本）."

I had been to Japan.在過去的某個時間點之前曾經去過日本，一定是在描述過去某個情境的時候使用。例如：Tommy asked me how many countries I had visited, I said I had only been to Japan. （湯米問我去過幾個國家，我說我只去過日本。）

假如人家問："How many countries have you visited?（你去過幾個國家?）" ，你回答"I had only been to Japan"，那這句話文法是錯誤的，不過對方還是能猜得到意思。也沒有have been跟had been意思不一樣的問題，因為他們兩個的意思其實一模一樣，沒有啥語氣強烈的區分，純粹是時態不同而已。