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I'm trying to use the pop-up footnotes for that are now supported by iBooks see here. I can get the pop ups to work and it has the text that I want, but for some reason the text in the aside is also showing.

Why does it do that? I can't tell what I'm doing differently compared to the examples that I've seen. I put my markup below. I've also taken screen shots of my computer so that you can see what I'm talking about. See here and here

<html xmlns="http://www.w3.org/1999/xhtml" xmlns:epub="http://www.idf.org/2007/ops">
<head>
    <meta charset="utf-8"/>
    <title>Hello World: My First EPUB</title>
    <link type="text/css" rel="stylesheet" media="all" href="stylesheet.css" />
</head>
<body>
  <p>
      Alice was beginning to get very tired of sitting by her sister on the bank, and of having nothing to do: once or twice she had peeped into the book her sister was reading, but it had no pictures or conversations in it, 'and what is the use of a book,' thought Alice 'without pictures or conversation?'
      <a href="content.html#l13" epub:type="noteref">1</a>
  </p>
  <aside id="l13" epub:type="footnote">Alice estava começando a ficar muito cansada de sentar-se ao lado de sua irmã no banco e de não ter nada para fazer: uma ou duas vezes havia espiado o livro que a irmã estava lendo, mas não havia imagens nem diálogos nele, "e para que serve um livro", pensou Alice, "sem imagens nem diálogos?"
  </aside>

  <p>
    <a href="content.html#l24" epub:type="noteref">So she was considering in her own mind (as well as she could, for the hot day made her feel very sleepy and stupid), whether the pleasure of making a daisy-chain would be worth the trouble of getting up and picking the daisies, when suddenly a White Rabbit with pink eyes ran close by her.
    </a>
  </p>
  <aside id="l24" epub:type="footnote">Então, ela pensava consigo mesma (tanto quanto podia, uma vez que o dia quente a fazia sentir-se sonolenta e letárgica) se o prazer de fazer uma coroa de margaridas valeria o trabalho de se levantar e apanhá-las, quando repentinamente um Coelho Branco com olhos rosados passou correndo perto dela.
  </aside>

  </body>
</html>
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  • Setting visibility to hidden hides footnote in popup too. Have you found any solution? – Heidar Jun 14 '15 at 15:07
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First of all, note that iBooks for OS X is very very buggy, and its behavior differs from iBooks on iOS with respect to many functions.

Said that, note that "iBooks hiding <aside> elements" is an Apple quirk; any other reading system, in absence of relevant CSS rules or if they don't have a specialized behavior on elements carrying an epub:type, will display an <aside> as any other <div>.

Have you tried applying a CSS rule (e.g., visibility: hidden) to your <aside>?

BTW, for compatibility reasons, I tend to group the notes at the end of the XHTML file.

Some links you might find useful:

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