1
#header{
  margin: 0px;
  padding: 0px;
  border: 0px;
  width:100%;
  height:100px;
  background-color:#00F;
}
  
#conteudo{
  widows: 100%;
  margin: 0px;
  padding: 0px;
  border: 0px;
  height:500px;
  background-color:#0F0;
}
#footer{
  widows: 100%;
  padding: 0px;
  border: 0px;
  margin: 0px;
  height:100px;
  background-color:#C3C;
}
#Conteudo-Top{
  widows: 100%;
  margin: 0px;
  padding: 0px;
  border: 0px;
  height:250px;
  background-color:red;
}
 #Conteudo-Down{
  margin: 0px;
  padding: 0px;
  border: 0px;
  widows: 100%;
  height:250px;
  background-color:blueviolet;
 }<div id="site">
  <div id="header"><h1>Header</h1></div>
  <div id="conteudo">
  <div id="Conteudo-Top"><h1>Conteudo TOP</h1></div>
  <div id="Conteudo-Down"><h1>Conteudo Down</h1></div>
  <div id="footer"><h1>Footer</h1></div>
</div>
Why - I believe it has something to do with the font size of the document. Use the universal selector by applying font-size:0; the spaces will disappear
– user60252