Align inline-block DIVs to top of container element

Because the vertical-align is set at baseline as default.

Use vertical-align:top instead:

.small{
    display: inline-block;
    width: 40%;
    height: 30%;
    border: 1px black solid;
    background: aliceblue;   
    vertical-align:top; /* <---- this */
}

http://jsfiddle.net/Lighty_46/RHM5L/9/

Or as @f00644 said you could apply float to the child elements as well.

You need to add a vertical-align property to your two child div's.

If .small is always shorter, you need only apply the property to .small. However, if either could be tallest then you should apply the property to both .small and .big.

.container{ 
    border: 1px black solid;
    width: 320px;
    height: 120px;    
}

.small{
    display: inline-block;
    width: 40%;
    height: 30%;
    border: 1px black solid;
    background: aliceblue; 
    vertical-align: top;   
}

.big {
    display: inline-block;
    border: 1px black solid;
    width: 40%;
    height: 50%;
    background: beige; 
    vertical-align: top;   
}

Vertical align affects inline or table-cell box's, and there are a large nubmer of different values for this property. Please see https://developer.mozilla.org/en-US/docs/Web/CSS/vertical-align for more details.